For $2400 I would hope they are blasting it, either dry ice or some other media. If that is the case, $2,400 actually isn't bad. Would also be worth asking them what their "paint and seal" process is. Are they just painting with a Rustoleum type product, or are they using a true rust encapsulator and then painting? Either way, there's no guarantee that it won't come back. Some of that rust is pretty deep into metal and will surface again, sooner rather than later if you're staying in the Northeast. Definitely do fluidfilm before winter. As for your body rust, where there's smoke there's fire. If you're cleaning off rust stains with WD40, the stains came from somewhere, so be prepared for those to start coming through the paint soon.
At the end of the day, you gotta ask yourself what you're really trying to do with the truck. You can go back a few pages and see my purchase. I paid a lot for truck that turned out to be pretty crusty in places. Overall it's not bad, but has body rust in a couple spots. I was quoted $2300 by a reputable shop to cut it out and repair/paint. I'm still on the fence with that as well, but with the rest of the truck being rock solid, I am planning on leaving the body rust for a couple years, building out the suspension and upgrading everything else first, then I'll deal with the body later, considering there is always a chance I'm going to bash it up anyway. Besides, the body is purely cosmetic.